A woman's body does NOT keep producing eggs until menopause. However, eggs from only one of Sydney's ovaries were harvested; the other was untouched, which means that it is completely possible for Sydney to get pregnant like anybody else.
I don't think having a baby is a bad career move for JG, and frankly, I think it's beyond crass to describe having a child in that way. And unless you know Ben Affleck -- JG does, we don't -- you're in no position to judge his capacity to be a father and husband. (Maybe he's wonderful. Maybe he's awful. We don't know, and our opinions don't matter.)
I think they pretty much have to write it in. I think it is a gamble, but OTOH, some shows have done it brilliantly. "The X-Files" did its best story arc ever to accommodate GA's pregnancy, after all. And Sydney has to be central to "Alias" -- she is the lead character, and her being the focus of the drama is more important than her wearing tight clothes, being an action star, etc. As Sydney will not be able to be the focus in the same way as she has in the past (others will have to pick up the action parts), the only way to keep Sydney at the focus of the story is to write a major, non-action-oriented plotline for her. A pregnancy storyline would do this, and would have effects on the rest of the characters (Vaughn, Jack, Nadia, Sloane, various Rambaldi cultists, etc.), plus explain why she's not in the field all the time. So I think it's probably the best option.
ETA: I think the only other plotline that would keep Sydney at the center of the story AND explain her absences/not being in the field would be an abduction storyline -- Sark or Elena or someone takes her captive, and she's missing for several episodes. This might be feasible, but IMHO, it's even riskier than than the pregnancy in terms of holding viewer interest, and would probably result in us seeing a lot less of Sydney overall than a pregnancy storyline would.
